Problems with fix wall/harmonic

Hello,

My simulation involves a polymer chain and a crystal over which the chain
should be crystallized. I want to create walls on four sides of the
simulation box to make sure the chain interacts with only that surface. I
used fixed boundary conditions for all three dimensions and fix
wall/harmonic command to create a wall.

fix walllj chains wall/harmonic xlo -5 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic xhi -95 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zlo -8 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zhi 100 20.0 2.0 12.5 units box

My simulation box dimension:

-6 +96 xlo xhi
-51 +51 ylo yhi
-9 +101 zlo zhi

When I start the simulation, it runs for a while and when the polymer
chain comes too close to the face of my simulation box, it doesn't
interact with the harmonic wall and just pass through it. I get an error
"ERROR on proc 4: Bond atoms 290 291 missing on proc 4 at step 932628
(../neigh_bond.cpp:65)"

Can anyone tell me what my mistake is?

Hello,

My simulation involves a polymer chain and a crystal over which the chain
should be crystallized. I want to create walls on four sides of the
simulation box to make sure the chain interacts with only that surface. I
used fixed boundary conditions for all three dimensions and fix
wall/harmonic command to create a wall.

​​
fix walllj chains wall/harmonic xlo -5 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic xhi -95 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zlo -8 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zhi 100 20.0 2.0 12.5 units box

My simulation box dimension:

-6 +96 xlo xhi
-51 +51 ylo yhi
-9 +101 zlo zhi

When I start the simulation, it runs for a while and when the polymer
chain comes too close to the face of my simulation box, it doesn't
interact with the harmonic wall and just pass through it. I get an error
"ERROR on proc 4: Bond atoms 290 291 missing on proc 4 at step 932628
(../neigh_bond.cpp:65)"

Can anyone tell me what my mistake is?

​you are using the same fix id for all your fix wall commands. this way the
next wall definition will ​overwrite the previous one and thus your system
has only one wall instead of four. please re-read the documentation for the
fix command carefully: http://lammps.sandia.gov/doc/fix.html

axel.

oh, and you can confirm this, by adding the command “info fixes” to your input and checking the corresponding output. http://lammps.sandia.gov/doc/info.html

axel.